Can not run ClinSV in Singularity

[weizhousjtu]

Dear Andre,

I installed Singularity by root and download clinsv.sif, refdata and NA12878_v0.9.bam as suggested. Then I run the following code:

$singularity run clinsv.sif \ -i "$input_path/*.bam" \ -ref $refdata_path \ -p $Out_path/project_folder
The error is :

error exist status != 0 (512), please check /home/zhouwei/zhou_data/WGS/CHD_Trio_WGS//project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e for more information

I check the 'bigwig.createWigs.FR05812606.e' file and found

`

• export PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• cd /home/project_folder/alignments/FR05812606/bw/
• sort -k2,2nr /home/RefData/reference/b37/clinsv/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai
• awk '{print $1":1-"$2}'
• xargs -P 15 -t '-i{}' perl /opt/clinsv/clinSV/scripts/bam2wig.pl 1 q0 '{}' /home/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0 /home/RefData/reference/b37/clinsv/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta /home//project_folder/alignments/FR05812606/FR05812606.bam
  sort: open failed: /home/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai: No such file or directory
  `

However, it worked when I run:
sort -k2,2nr /home//clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai

I noticed that

export PATH=/opt/clinsv/bin

However, my "clinsv.sif" file and Singularity file is not located in that path.

Does this cause the error?
How do I set the corrected path of clinsv?

Thank you!

LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.2.1511 (Core)
Release: 7.2.1511

[MinocheAE]

regarding: "sort: open failed: /home/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai:"
Looks like a path issue. Try using absolute paths.
Did you follow these examples exactly?
https://github.com/KCCG/ClinSV#download
https://github.com/KCCG/ClinSV#using-singularity

clinsv.sif does not need to be in path, just in the directory where you are currently at.

[weizhousjtu]

Thank you for your suggestions.
However, I have another error when I run the following code.
`refdata_path=$PWD/clinsv/refdata-b37
input_path=$PWD

singularity run clinsv.sif
-i "$input_path/*.bam"
-ref $refdata_path
-p $PWD/project_folder
I checked theGLIBC_2.14' in my system
strings /lib64/libc.so.6 | grep GLIBC
and I found `GLIBC_2.14' already available

My system is Linux version 3.10.0-1062.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36)

[weizhousjtu]

sorry, the error is
/bin/sh: /lib64/libc.so.6: version GLIBC_2.14' not found (required by /opt/xalt/xalt/lib64/libxalt_init.so)`

[drmjc]

thanks for reporting this issue, but we haven't seen this error. the GLIBC in your system may be different to the one running in the singularity container.

We are currently refactoring ClinSV and will run more testing, so hopefully this will ultimately correct this issue.